Except for simple, quick hacks, avoid SIGALRM.  It's a very old, limited mechanism, not suited to anything more complex: you can only set a single alarm, and it interrupts any system call at the time rather than just the one you intend to interrupt.
It's much cleaner to use a timeout thread to kill the process, for example:
import subprocess, signal, os, threading, errno
from contextlib import contextmanager
class TimeoutThread(object):
    def __init__(self, seconds):
        self.seconds = seconds
        self.cond = threading.Condition()
        self.cancelled = False
        self.thread = threading.Thread(target=self._wait)
    def run(self):
        """Begin the timeout."""
        self.thread.start()
    def _wait(self):
        with self.cond:
            self.cond.wait(self.seconds)
            if not self.cancelled:
                self.timed_out()
    def cancel(self):
        """Cancel the timeout, if it hasn't yet occured."""
        with self.cond:
            self.cancelled = True
            self.cond.notify()
        self.thread.join()
    def timed_out(self):
        """The timeout has expired."""
        raise NotImplementedError
class KillProcessThread(TimeoutThread):
    def __init__(self, seconds, pid):
        super(KillProcessThread, self).__init__(seconds)
        self.pid = pid
    def timed_out(self):
        try:
            os.kill(self.pid, signal.SIGKILL)
        except OSError as e:
            # If the process is already gone, ignore the error.
            if e.errno not in (errno.EPERM, errno. ESRCH):
                raise e
@contextmanager
def processTimeout(seconds, pid):
    timeout = KillProcessThread(seconds, pid)
    timeout.run()
    try:
        yield
    finally:
        timeout.cancel()
def example():
    proc = subprocess.Popen(["sleep", "5"], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
    with processTimeout(1, proc.pid):
        print proc.communicate()
    resultcode = proc.wait()
    if resultcode < 0:
        print "error: %i" % resultcode
if __name__ == '__main__':
    example()
Depending on what you're timing out, you may want to use a lighter signal than SIGKILL to allow the timing-out process to clean up after itself.